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- PDB-1ao7: COMPLEX BETWEEN HUMAN T-CELL RECEPTOR, VIRAL PEPTIDE (TAX), AND H... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ao7 | ||||||
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Title | COMPLEX BETWEEN HUMAN T-CELL RECEPTOR, VIRAL PEPTIDE (TAX), AND HLA-A 0201 | ||||||
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![]() | COMPLEX (MHC/VIRAL PEPTIDE/RECEPTOR) / CLASS I MHC / T-CELL RECEPTOR / VIRAL PEPTIDE / COMPLEX (MHC-VIRAL PEPTIDE-RECEPTOR / COMPLEX (MHC-VIRAL PEPTIDE-RECEPTOR) COMPLEX | ||||||
Function / homology | ![]() symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / T cell mediated cytotoxicity directed against tumor cell target / T cell receptor complex / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation ...symbiont-mediated perturbation of host exit from mitosis / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / T cell mediated cytotoxicity directed against tumor cell target / T cell receptor complex / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / regulation of mRNA stability / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / SH3 domain binding / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / ER-Phagosome pathway / iron ion transport / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / cellular response to lipopolysaccharide / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / host cell cytoplasm / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Garboczi, D.N. / Ghosh, P. / Utz, U. / Fan, Q.R. / Biddison, W.E. / Wiley, D.C. | ||||||
![]() | ![]() Title: Structure of the complex between human T-cell receptor, viral peptide and HLA-A2. Authors: Garboczi, D.N. / Ghosh, P. / Utz, U. / Fan, Q.R. / Biddison, W.E. / Wiley, D.C. #1: ![]() Title: Assembly, Specific Binding, and Crystallization of a Human Tcr-Alphabeta with an Antigenic Tax Peptide from Human T Lymphotropic Virus Type 1 and the Class I Mhc Molecule Hla-A2 Authors: Garboczi, D.N. / Utz, U. / Ghosh, P. / Seth, A. / Kim, J. / Vantienhoven, E.A. / Biddison, W.E. / Wiley, D.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156.5 KB | Display | ![]() |
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PDB format | ![]() | 122.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 477.1 KB | Display | ![]() |
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Full document | ![]() | 494.6 KB | Display | |
Data in XML | ![]() | 27.9 KB | Display | |
Data in CIF | ![]() | 37.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31854.203 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS ALPHA 1, ALPHA 2, ALPHA 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Cellular location (production host): REFOLDED FROM INCLUSION BODIES Production host: ![]() ![]() |
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#2: Protein | Mass: 11793.288 Da / Num. of mol.: 1 / Mutation: Y67C, K91C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Cellular location (production host): REFOLDED FROM INCLUSION BODIES Production host: ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1070.280 Da / Num. of mol.: 1 Fragment: RESIDUES 11 - 19 FROM TAX PROTEIN OF HUMAN T LYMPHOTROPIC VIRUS TYPE 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
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-T CELL RECEPTOR ... , 2 types, 2 molecules DE
#4: Protein | Mass: 22488.549 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS V AND C, RESIDUES 1 - 212 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Cellular location (production host): REFOLDED FROM INCLUSION BODIES Production host: ![]() ![]() |
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#5: Protein | Mass: 27360.379 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS V AND C, RESIDUES 1 - 246 / Mutation: C191A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: V BETA 12.3 [BV13S1] - D BETA 2.1 - J BETA 2.1 - C BETA 2 Organ: PLASMA / Plasmid: PLM1 / Species (production host): Escherichia coli Cellular location (production host): REFOLDED FROM INCLUSION BODIES Production host: ![]() ![]() |
-Non-polymers , 2 types, 39 molecules ![](data/chem/img/EMC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 56 % |
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Crystal grow | pH: 6.5 Details: CRYSTALLIZED FROM 10% PEG 8000, 100 MM MGACETATE, 50 MM NACACODYLATE, PH 6.5 |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: May 5, 1996 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.914 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→12 Å / Num. obs: 29279 / % possible obs: 95 % / Observed criterion σ(I): -3.5 / Redundancy: 3.1 % / Biso Wilson estimate: 48.5 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.246 / % possible all: 82.9 |
Reflection shell | *PLUS % possible obs: 82.9 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1HHK, 1BEC CHAIN 1934.4 Resolution: 2.6→6 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1000000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: REFMAC ALSO USED FOR REFINEMENT.
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Displacement parameters | Biso mean: 42.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.71 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.359 |